There are certainly some differences. DOS is a a category of operating system, albeit a very old and simple one (compared to today). MS-DOS was the Microsoft version, although there were several others. Since it did more than run commands (dir, cls, etc.) which is what the command prompt does, I'd say they are different.

On a somewhat related note, some machines at one of the buildings my dad inspects still use MS-DOS to run their security system.

Free-DOS is pretty cool ( http://www.freedos.org/ ) i used to use Free-DOS to PXE boot over LAN some boot strapped DOS programs such as Norton Ghost when i got my first Systems Administration gig ..... god i sooooo don't miss being a systems administrator.

"If art interprets our dreams, the computer executes them in the guise of programs!" - SICP

“If at first, the idea is not absurd, then there is no hope for it” - Albert Einstein